Sequence
atgc intronic sequence ATGC exonic sequence...ccattcccaccattgaattattggattttagtcttatggttttgtgaatgaagtcacttcagtttctttgatgcaataacattacttgttcaatatgtagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACTGACAAATATGGTGGATCCCT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0041g02060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA01G44600.1 (Glycine max), 3'ss of exon 3
-ccattcccaccattgaattattggattttagtcttatggttttgtgaatgaagtcacttcagtttctttgatgcaataacattacttgttcaatatgtagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACTGACAAATATGGTGGATCCCT
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gtaatttcccccacc------ttttgctcctgccaaatactaatgtttcaaataccctgccaaatact--aacatcatatccatggctgtgcaaattgtagGTTTTGATGGGGTTGAGATCCATGGGGCTCATGGCTACCTGCTTGAGCAATTTATGAAAGATAAAGTGAATGACCGAACAGACGAATATGGTGGATCCCT
upper sequence: Vv18s0041g02060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA11G00980.1 (Glycine max), 3'ss of exon 4
ccattcccaccattgaattattggattttagtcttatggttttgtgaatgaagtcacttcagtttctttgatgcaataacattacttgttcaatatgtagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACTGACAAATATGGTGGATCCCT
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--------gtaattt--cccttcccttttgctcctacaaatgt-tctttcaaattgttttacaaactagactagcatacccgtggttgtgcaaattatagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGTTACCTTATTGATCAATTCCTGAAAGATAAGGTGAATGACCGAACAGACCAATATGGTGGATCCCT
upper sequence: Vv18s0041g02060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G09320.1 (Glycine max), 3'ss of exon 4
----ccattcccaccattgaattattggattttagtcttatggttttgtgaatgaagtcacttcagtttctttgatgcaataacattacttgt---tcaatatgtagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACTGACAAATATGGTGGATCCCT
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gtaatttgcctggaaaacaaaatttcacacacatgtactaagatctttaaattttacataatatgaaatgt--aatgtaagtatctaacatacaaatccatgtgtagGTTTTGATGGGGTTGAGATCCACGGTGCTCATGGCTACTTACTTGAGCAATTCATTAAAGACAAAGTGAATGATCGAAGTGATGGATATGGTGGATCCCT
upper sequence: Vv18s0041g02060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA15G35410.1 (Glycine max), 3'ss of exon 4
ccattcccaccattgaattattggattttagtcttatggttttg----tgaatgaagtcacttcagtttctttgatgcaataacattacttgttcaatatgtagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACTGACAAATATGGTGGATCCCT
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tcatatacctgagtggagtttcactttaatatgatatagtcatgatgttaaactgtgattctcaaagatattcaattcc-taaccgcaattg--caat-tgtagGGTTTGATGGAGTTGAGATACATGGGGCACATGGTTTTCTAATTGATCAGTTTTTGAAAGATCAAGTTAACGACAGAACAGACAAATATGGTGGATCCAC
upper sequence: Vv18s0041g02060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G25570.1 (Glycine max), 3'ss of exon 4
ccattcccaccattgaattattggattttagtct-tatggttttgtgaatgaagtcacttcagtttctttgatgcaataacattacttgttcaata----------tgtagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACTGACAAATATGGTGGATCCCT
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--------atgagtgga--gttgcactttaatgtatatgatatag-gcatgatgttaaactgggattttcgaattaagttcatcaattcctaaccacaattgcaattgtagGGTTTGATGGAGTTGAGATCCATGGGGCACATGGTTTTCTAATTGATCAATTTTTGAAAGACCAAGTTAACGACAGAACAGACAAATACGGTGGATCATT
upper sequence: Vv18s0041g02060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ20558 (Selaginella moellendorffii), 3'ss of exon 4
ccattcccaccattgaattattggattttagtcttatggttttgtgaatgaagtcacttcagtttctttgatgcaataacattacttgtt-caatatgtagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACTGACAAATATGGTGGATCCCT
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-------------------------------------------gtgttaaactatgcttctttctttctagtttcatgggctaacgaaaaactgggtgtagGCTTTGATGGTGTTGAGATCCATGGGGCTCACGGCTATCTGATCGACCAATTCCTGAAAAATGGTGTCAACGATAGAACGGATGAGTATGGTGGTTCTTT
upper sequence: Vv18s0041g02060.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: EFJ28624 (Selaginella moellendorffii), 3'ss of exon 4
ccattcccaccattgaattattggattttagtcttatggttttgtgaatgaagtcacttcagtttctttgatgcaataacattacttgtt-caatatgtagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACTGACAAATATGGTGGATCCCT
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-------------------------------------------gtgttaaactatgcttctttctttctagtttcacaggctaacgaaaaactgggtgtagGCTTTGATGGTGTTGAGATCCACGGGGCTCACGGCTATCTGATCGACCAATTCCTGAAAGATGGTGTCAACGATAGAACGGATGAGTACGGTGGTTCTCTMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|161716760|gb|FC065583.1|FC065583EST: TCAAGTTGTAAAGGATTTTAGACTTGCTGCAAGGAACGCTATTGAAGCTG GTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGT
genomic: TCAAGTTGTAAAGGATTTTAGACTTGCTGCAAGGAACGCTATTGAAGCTGgtatgtgata ... caatatgtagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatgaagtcacttcagtttctttgatgcaataacattacttgttcaatatgtagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACTGACAAATATGGTGGATCCCT
caataac putative branch site (score: 2)
cttgttc putative PPT
aataacatta TA-rich tract
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccattcccaccattgaattattggattttagtcttatggttttgtgaatgaagtcacttcagtttctttgatgcaataacattacttgttcaatatgtagGTTTTGATGGAGTTGAGATCCATGGGGCTCATGGCTACCTACTTGACCAGTTCATGAAAGACCAGGTCAATGATCGAACTGACAAATATGGTGGATCCCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA